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Molecular Dynamics Simulations of RNA Motifs to Guide the Architectural Parameters and Design Principles of RNA Nanostructures

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RNA Nanostructures

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2709))

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Abstract

Molecular dynamics (MD) simulations can be used to investigate the stability and conformational characteristics of RNA nanostructures. However, MD simulations of an RNA nanostructure is computationally expensive due to the size of nanostructure and the number of atoms. Alternatively, MD simulations of RNA motifs can be used to estimate the conformational stability of constructed RNA nanostructure due to their small sizes. In this chapter, we introduce the preparation and MD simulations of two RNA kissing loop (KL) motifs, a linear KL complex and a bent KL complex, and an RNA nanoring. The initial solvated system and topology files of each system will be prepared by two major force fields, AMBER and CHARMM force fields. MD simulations will be performed by NAMD simulation package, which can accept both force fields. In addition, we will introduce the use of the AMBER cpptraj program and visual molecular dynamics (VMD) for data analysis. We will also discuss how MD simulations of two KL motifs can be used to estimate the conformation and stability of RNA nanoring as well as to explain the vibrational characteristics of RNA nanoring.

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Authors and Affiliations

  1. Physical Sciences Department, West Virginia University Institute of Technology, Beckley, WV, USA

    Valentina Abondano Perdomo & Taejin Kim

Authors
  1. Valentina Abondano Perdomo
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  2. Taejin Kim
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Correspondence to Taejin Kim .

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Editors and Affiliations

  1. Department of Chemistry, UNC Charlotte, Charlotte, NC, USA

    Kirill A. Afonin

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Perdomo, V.A., Kim, T. (2023). Molecular Dynamics Simulations of RNA Motifs to Guide the Architectural Parameters and Design Principles of RNA Nanostructures. In: Afonin, K.A. (eds) RNA Nanostructures. Methods in Molecular Biology, vol 2709. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3417-2_1

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  • DOI: https://doi.org/10.1007/978-1-0716-3417-2_1

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3416-5

  • Online ISBN: 978-1-0716-3417-2

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